Package | Description |
---|---|
com.compomics.util.exceptions.exception_handlers |
Implementations of the ExceptionHandler interface.
|
com.compomics.util.experiment.identification.protein_inference.proteintree |
Protein sequence database indexing classes.
|
com.compomics.util.experiment.identification.protein_sequences |
Protein sequence handling related classes.
|
Modifier and Type | Class and Description |
---|---|
class |
CommandLineExceptionHandler
Exception handler for command line processes.
|
class |
FrameExceptionHandler
Handles exception for a given application and displays warnings using
dialogs.
|
class |
WaitingDialogExceptionHandler
Exception handler for processes making use of a waiting dialog.
|
Modifier and Type | Method and Description |
---|---|
void |
ProteinTree.initiateTree(int initialTagSize,
int maxNodeSize,
int maxPeptideSize,
Enzyme enzyme,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler,
boolean printExpectedImportTime,
boolean displayProgress,
int nThreads)
Initiates the tree.
|
void |
ProteinTree.initiateTree(int initialTagSize,
int maxNodeSize,
int maxPeptideSize,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler,
boolean printExpectedImportTime,
boolean displayProgress,
int nThreads)
Initiates the tree.
|
Modifier and Type | Method and Description |
---|---|
PeptideMapper |
SequenceFactory.getDefaultPeptideMapper(SequenceMatchingPreferences sequenceMatchingPreferences,
SearchParameters searchParameters,
PeptideVariantsPreferences peptideVariantsPreferences,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler)
Returns the default peptide to protein mapper for the database loaded in
factory according to the sequence matching preferences.
|
PeptideMapper |
SequenceFactory.getDefaultPeptideMapper(SequenceMatchingPreferences sequenceMatchingPreferences,
SearchParameters searchParameters,
PeptideVariantsPreferences peptideVariantsPreferences,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler,
boolean displayProgress,
int nThreads)
Returns the default peptide to protein mapper for the database loaded in
factory according to the sequence matching preferences.
|
PeptideMapper |
SequenceFactory.getDefaultPeptideMapper(WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler,
int nThreads,
IdentificationParameters identificationParameters)
Returns the default peptide to protein mapper for the database loaded in
factory according to the sequence matching preferences.
|
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